We have a small 40 foot long 12 foot wide 7 foot high poly tunnel that is currently housing our chickens for the winter.
We plan on blocking off 2/3 of it for seed starring.

We are zone 4 northern vermont. So I was going to build a few small raised beds with a mini green house with in a greenhouse. Is this doable in winter or should I start them inside which we are trying to avoid, hence the poly tunnel. Thoughts?

Eliot Coleman has been trialing all sorts of things using this exact method. He has large hoop houses similar to what you have and then he uses row fabric to cover individual beds for an added layer of protection. The first hoop house keeps things mostly frost free except on the really cold nights. The row fabric on the beds adds an extra 10 degrees or so of protection. I know he's used this method here in Maine for growing carrots and some greens through the winter. The only drawback is that for every layer of cold protection you have, you lose a little light getting to the plants. It's a trade off. One other thing about onions is that they are day length sensitive so be sure to check you varieties of onions on that.

I say it's totally doable and with many more crops than just the onions.

Elliot Coleman's Four Season Harvest book has great charts on when to plant based on what season extenders and USDA zone you are in. He has done his research in coastal Maine.

http://smile.amazon.com/Four-Season-Harvest-Organic-Vegetables-Garden/dp/1890132276/ref=sr_1_1?ie=UTF8&qid=1423020516&sr=8-1&keywords=four+season+harvest